An allele-specific expression atlas across bovine breeds and multiple tissues

Allele-specific expression (ASE) analysis, when integrated with eQTL mapping, selective sweep analyses, and phenotypic data, provides a powerful approach for prioritizing candidate adaptive variants underlying complex traits. This study integrates 234 genomic datasets and 623 transcriptomic datasets across seven tissues from 32 diverse Bovini breeds and populations to investigate evolutionary shifts in gene expression. We generated an ASE map across ancestries and tissues, including 10 domestic cattle breeds (nine indigenous breeds from Yunnan and one introduced breed), Zhongdian yak (Bos grunniens), and Yunnan gayal (Bos frontalis), and systematically characterized ASE variants at the individual, breed, and population levels. Furthermore, by integrating ASE variants with functional genomic data (e.g., ChIP-seq and Hi-C) and 1,028 phenotypic records (including traits such as muscle fiber diameter and relative hump weight), this dataset enables exploration of the potential roles and regulatory mechanisms of ASE in environmental adaptation in cattle. Overall, this resource expands current knowledge of cis-regulatory variation in Bovini species and provides a valuable foundation for future studies on gene regulation and adaptive evolution.